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Very high LJ interactions
- bond_007
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3 years 11 months ago #8547
by bond_007
Very high LJ interactions was created by bond_007
Hello,
I am simulation two protein chains (app 214 residues each) with the std. MARTINI water model and I am observing very high LJ energies.
For comparision these are the averages for the other terms:
Bond: 2700 kJ/mol
Angle: 280 kJ/mol
Improper Dih. : 1.5 kJ/mol
Coulomb : - 1500 kJ/mol
LJ : -3177963.5 kJ/mol
Because of this my pot. energies are are getting skewed. Is this normal for the MARTINI force-field or is there something wring with my system or .mdp file?
Thanks!
I am simulation two protein chains (app 214 residues each) with the std. MARTINI water model and I am observing very high LJ energies.
For comparision these are the averages for the other terms:
Bond: 2700 kJ/mol
Angle: 280 kJ/mol
Improper Dih. : 1.5 kJ/mol
Coulomb : - 1500 kJ/mol
LJ : -3177963.5 kJ/mol
Because of this my pot. energies are are getting skewed. Is this normal for the MARTINI force-field or is there something wring with my system or .mdp file?
Thanks!
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- vainikka
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3 years 11 months ago #8559
by vainikka
Replied by vainikka on topic Very high LJ interactions
Hi,
The LJ energy term is usually quite large, but it's impossible to dictate whether or not your case is abnormal, if you do not provide any further information. I suppose the easiest thing to do is to assess if the system behaving normally.
The LJ energy term is usually quite large, but it's impossible to dictate whether or not your case is abnormal, if you do not provide any further information. I suppose the easiest thing to do is to assess if the system behaving normally.
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3 years 10 months ago #8575
by bond_007
Replied by bond_007 on topic Very high LJ interactions
Thanks for the reply.
I don't have a reason to suspect that my system is behaving abnormally. But what kind of further information would you require to judge if these high LJ energies are actually wrong?
I don't have a reason to suspect that my system is behaving abnormally. But what kind of further information would you require to judge if these high LJ energies are actually wrong?
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3 years 10 months ago #8576
by vainikka
Replied by vainikka on topic Very high LJ interactions
Hi,
If you don't see any unexpected behaviour, such as freezing water etc, then I wouldn't worry.
And with further information I wanted to point out that on it's own the LJ energy term is just a number, which doesn't really tell me anything without context (e.g. does it fluctuate wildly, do other energy terms behave weirdly, does your water freeze, etc.)
If you don't see any unexpected behaviour, such as freezing water etc, then I wouldn't worry.
And with further information I wanted to point out that on it's own the LJ energy term is just a number, which doesn't really tell me anything without context (e.g. does it fluctuate wildly, do other energy terms behave weirdly, does your water freeze, etc.)
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